Generic placeholder image

Current Proteomics

Author(s): Neelja Singhal, Anjali Garg, Nirpendra Singh, Manish Kumar and Manisha Goel*

DOI: 10.2174/1570164619666220429121247

DownloadDownload PDF Flyer Cite As
Proteomics and Computational Analysis of Cytosolic Proteome of a Thermoacidophilic Euryarchaeon, Picrophilus torridus

Page: [290 - 298] Pages: 9

  • * (Excluding Mailing and Handling)

Abstract

Background: Picrophilus torridus is a thermoacidophilic archaeon that thrives in an extremely low pH (0-1) and high temperatures (50-60°C). Thus, it is a suitable organism to study microbial genetics and metabolic adaptations to the extremely acidic and moderate thermal environment.

Objective: In the present study we have conducted a global proteome analysis of P. torridus and discerned the cytosolic proteome of P. torridus using gel-free, liquid chromatographymass spectrometry (LC-MS/MS).

Methods: The cytosolic proteins of P. torridus were extracted and identified using gel-free, LCMS/ MS. Gene Ontology-based pathway analysis and protein-protein interaction studies were performed to understand the role of various cytosolic proteins in sustaining the thermoacidophilic environment. Also, domain analysis of hypothetical/uncharacterized proteins was performed.

Results: Using gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, including 36 hypothetical/uncharacterized proteins. Thus, we could identify 26.58 % of the theoretical proteome of P. torridus. The majority of the cytosolic proteins were observed to be multi-functional and involved in activities related to microbial metabolism.

Conclusion: Comparison with an earlier study that used gel-based LC-MS analysis to identify cytosolic proteins of P. torridus revealed that gel-free LC-MS was better in identifying more number of proteins and also, higher/lower molecular weight proteins. The findings of this study may contribute to our understanding of the P. torridus proteome and serve as a foundation for future proteomic research on other thermoacidophilic archaea.

Keywords: Thermoacidophilic, liquid chromatography-mass spectrometry, cytosolic proteins, archaea, proteome, computational analysis.

Graphical Abstract

[1]
Leigh, J.A.; Albers, S.V.; Atomi, H.; Allers, T. Model organisms for genetics in the domain Archaea: Methanogens, halophiles, Thermo-coccales and sulfolobales. FEMS Microbiol. Rev., 2011, 35(4), 577-608.
[http://dx.doi.org/10.1111/j.1574-6976.2011.00265.x] [PMID: 21265868]
[2]
Lee, A.M.; Sevinsky, J.R.; Bundy, J.L.; Grunden, A.M.; Stephenson, J.L. Jr. Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods. J. Proteome Res., 2009, 8(8), 3844-3851.
[http://dx.doi.org/10.1021/pr801119h] [PMID: 19425607]
[3]
Tebbe, A.; Klein, C.; Bisle, B.; Siedler, F.; Scheffer, B.; Garcia-Rizo, C.; Wolfertz, J.; Hickmann, V.; Pfeiffer, F.; Oesterhelt, D. Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation. Proteomics, 2005, 5(1), 168-179.
[http://dx.doi.org/10.1002/pmic.200400910] [PMID: 15619297]
[4]
Kirkland, P.A.; Humbard, M.A.; Daniels, C.J.; Maupin-Furlow, J.A. Shotgun proteomics of the haloarchaeon Haloferax volcanii. J. Proteome Res., 2008, 7(11), 5033-5039.
[http://dx.doi.org/10.1021/pr800517a] [PMID: 18816081]
[5]
Liu, H.; Luo, Y.; Han, J.; Wu, J.; Wu, Z.; Feng, D.; Cai, S.; Li, M.; Liu, J.; Zhou, J.; Xiang, H. Proteome reference map of Haloarcula hispanica and comparative proteomic and transcriptomic analysis of polyhydroxyalkanoate biosynthesis under genetic and environmental perturbations. J. Proteome Res., 2013, 12(3), 1300-1315.
[http://dx.doi.org/10.1021/pr300969m] [PMID: 23301558]
[6]
Thombre, R.S.; Shinde, V.D.; Oke, R.S.; Dhar, S.K.; Shouche, Y.S. Biology and survival of extremely halophilic archaeon Haloarcula marismortui RR12 isolated from Mumbai salterns, India in response to salinity stress. Sci. Rep., 2016, 6(1), 25642.
[http://dx.doi.org/10.1038/srep25642] [PMID: 27231230]
[7]
Schleper, C.; Puehler, G.; Holz, I.; Gambacorta, A.; Janekovic, D.; Santarius, U.; Klenk, H.P.; Zillig, W. Picrophilus gen. nov., fam. nov.: A novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0. J. Bacteriol., 1995, 177(24), 7050-7059.
[http://dx.doi.org/10.1128/jb.177.24.7050-7059.1995] [PMID: 8522509]
[8]
Thürmer, A.; Voigt, B.; Angelov, A.; Albrecht, D.; Hecker, M.; Liebl, W. Proteomic analysis of the extremely thermoacidophilic archaeon Picrophilus torridus at pH and temperature values close to its growth limit. Proteomics, 2011, 11(23), 4559-4568.
[http://dx.doi.org/10.1002/pmic.201000829] [PMID: 22114103]
[9]
Lim, H.; Eng, J.; Yates, J.R., III; Tollaksen, S.L.; Giometti, C.S.; Holden, J.F.; Adams, M.W.; Reich, C.I.; Olsen, G.J.; Hays, L.G. Identification of 2D-gel proteins: A comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry. J. Am. Soc. Mass Spectrom., 2003, 14(9), 957-970.
[http://dx.doi.org/10.1016/S1044-0305(03)00144-2] [PMID: 12954164]
[10]
Arora, J.; Goswami, K.; Saha, S. Characterization of the replication initiator ORC1/CDC6 from the Archaeon Picrophilus torridus. J. Bacteriol., 2014, 196(2), 276-286.
[http://dx.doi.org/10.1128/JB.01020-13] [PMID: 24187082]
[11]
Kumar, R.; Singh, N.; Abdin, M.Z.; Patel, A.H.; Medigeshi, G.R. Dengue virus capsid interacts with DDX3X-a potential mechanism for suppression of antiviral functions in dengue infection. Front. Cell. Infect. Microbiol., 2018, 7, 542.
[http://dx.doi.org/10.3389/fcimb.2017.00542] [PMID: 29387631]
[12]
Singhal, N.; Garg, A.; Singh, N.; Gulati, P.; Kumar, M.; Goel, M. Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon. PLoS One, 2021, 16(8), e0255826.
[http://dx.doi.org/10.1371/journal.pone.0255826] [PMID: 34358261]
[13]
Camon, E.; Barrell, D.; Lee, V.; Dimmer, E.; Apweiler, R. The gene ontology annotation (GOA) database-an integrated resource of GO annotations to the UniProt knowledgebase. In silico Biol., 2004, 4(1), 5-6.
[PMID: 15089749]
[14]
Szklarczyk, D.; Morris, J.H.; Cook, H.; Kuhn, M.; Wyder, S.; Simonovic, M.; Santos, A.; Doncheva, N.T.; Roth, A.; Bork, P.; Jensen, L.J.; von Mering, C. The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res., 2017, 45(D1), D362-D368.
[http://dx.doi.org/10.1093/nar/gkw937] [PMID: 27924014]
[15]
Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 2000, 28(1), 27-30.
[http://dx.doi.org/10.1093/nar/28.1.27] [PMID: 10592173]
[16]
Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 2003, 13(11), 2498-2504.
[http://dx.doi.org/10.1101/gr.1239303] [PMID: 14597658]